ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.863-14C>T

gnomAD frequency: 0.00009  dbSNP: rs756001994
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000431533 SCV000514800 likely benign not specified 2015-11-17 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Color Diagnostics, LLC DBA Color Health RCV000579953 SCV000686696 likely benign Hereditary cancer-predisposing syndrome 2016-04-18 criteria provided, single submitter clinical testing
Invitae RCV002061530 SCV002338217 likely benign Peutz-Jeghers syndrome 2024-02-01 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV002061530 SCV004015577 likely benign Peutz-Jeghers syndrome 2023-07-07 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000431533 SCV004026955 likely benign not specified 2023-08-15 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV002061530 SCV004826215 likely benign Peutz-Jeghers syndrome 2023-12-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355315 SCV001550172 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The STK11 c.863-14C>T variant was not identified in the literature, nor was it identified in the Cosmic, LOVD 3.0, Zhejiang University Database, or Insight Hereditary Tumors databases. The variant was identified in dbSNP (ID: rs756001994 as "With Likely benign, Uncertain significance allele") and in ClinVar (2x as likely benign by GeneDx and Color Genomics). The variant was identified in control databases in 12 of 181762 chromosomes at a frequency of 0.00007 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 4 of 16456 chromosomes (freq: 0.0002), Other in 1 of 4832 chromosomes (freq: 0.0002), Latino in 3 of 25082 chromosomes (freq: 0.0001), European in 2 of 73216 chromosomes (freq: 0.00003), East Asian in 1 of 12088 chromosomes (freq: 0.00008), and South Asian in 1 of 22908 chromosomes (freq: 0.00004), while the variant was not observed in the Ashkenazi Jewish or Finnish populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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